But the public might not see any of the e-mails for quite some time because they will now go through the National Archives normal process for releasing presidential and agency records.
The tally of missing e-mails and the settlement are the latest development in a controversy surrounding the failure by the Bush White House to install a properly working electronic record keeping system.
The two private organizations - Citizens for Responsibility and Ethics in Washington and the National Security Archive - say there is not yet a final count on the extent of missing White House e-mail and there may never be a complete tally.
Meredith Fuchs, general counsel to the National Security Archive, said "many poor choices were made during the Bush administration and there was little concern about the availability of e-mail records despite the fact that they were contending with regular subpoenas for records and had a legal obligation to preserve their records."
"We may never discover the full story of what happened here," said Melanie Sloan, CREW's executive director. "It seems like they just didn't want the e-mails preserved."
Sloan said the latest count of misplaced e-mails "gives us confirmation that the Bush administration lied when they said no e-mails were missing."
The two groups say the 22 million White House e-mails were previously mislabeled and effectively lost.
The recovered e-mails - located over the past year by White House contractors - will now become part of the archived collection of papers at the National Archives and Records Administration.